[gmx-users] Sigma and epsilon parameters for water and graphene atoms

[Justin Lemkul]

On 7/31/16 11:21 AM, soumadwip ghosh wrote:
> Hi
>    In addition to my last query I would like to know whether the sigma
> values reported for CHARMM 27 are in Angstrom or in nm. Similarly, is the
> epsilon for atoms in kJ/mol or Kcal/mol? As of now, the values that I got

GROMACS uses SI.  See Chapter 2.

> from the ffnonbonded.itp in CHARMM 27 are 0 for TIP3P water's hydrogen. Is
> it right? Now if I want to report the graphene-water interaction should I

That's for standard TIP3P.  CHARMM should typically be used with the 
CHARMM-specific TIP3P, which has LJ terms on H atoms.  For folded proteins and 
nucleic acids, the effects are likely minimal, but for disordered states, use of 
the proper water model is significant.  NB for lipids, *always* use CHARMM TIP3P.

> take the sigma of CA atoms (carbon atoms in graphene) and water hydrogen
> and then find the arithmetic mean? Similarly, the geometric mean would give
> the epsilon? Is there anything wrong with this approach.Furthermore, in
> ffnonbonded.itp lines are written as below.
>

Looking only at H is incorrect.  Water O has LJ terms, and if you used standard 
TIP3P, these are actually the only interactions that matter in terms of LJ.

>
> [ atomtypes ]
> ;name   at.num  mass    charge  ptype   sigma   epsilon
> C       6       12.01100        0.51    A       0.356359487256  0.46024
> CA      6       12.01100        -0.115  A       0.355005321205  0.29288
> CC      6       12.01100        0.62    A       0.356359487256  0.29288
> CD      6       12.01100        0.000   A       0.356359487256  0.29288 ;
> partial charge def not found
> CE1     6       12.01100        0.000   A       0.372395664183  0.284512 ;
> partial charge def not found
> CE2     6       12.01100        0.000   A       0.370613866746  0.267776 ;
> partial charge def not found
> CM      6       12.01100        0.000   A       0.374177461619  0.46024 ;
> partial charge def not found
> CP1     6       12.01100        0.02    A       0.405358916754  0.08368
> CP2     6       12.01100        -0.18   A       0.387540942391  0.23012
> CP3     6       12.01100        0.00    A       0.387540942391  0.23012
> CPA     6       12.01100        0.000   A       0.320723538531  0.37656 ;
> partial charge def not found
> CPB     6       12.01100        0.000   A       0.320723538531  0.37656 ;
> partial charge def not found
> CPH1    6       12.01100        0.19    A       0.320723538531  0.2092
> CPH2    6       12.01100        0.32    A       0.320723538531  0.2092
> CPM     6       12.01100        0.000   A       0.320723538531  0.37656 ;
> partial charge def not found
> CPT     6       12.01100        -0.02   A       0.320723538531  0.37656
> CS      6       12.01100        0.000   A       0.391995435982  0.46024 ;
> partial charge def not found
> CST     6       12.01100        0.000   A       0.278494939291  0.242672 ;
> partial charge def not found
> CT1     6       12.01100        0.07    A       0.405358916754  0.08368
> CT2     6       12.01100        -0.18   A       0.387540942391  0.23012
> CT3     6       12.01100        -0.11   A       0.367050271874  0.33472
> CY      6       12.01100        -0.03   A       0.355005321205  0.29288
> CT      6       12.01100        0.000   A       0.405358916754  0.08368 ;
> partial charge def not found
> CT1x    6       12.01100        0.000   A       0.405358916754  0.08368 ;
> partial charge def not found
> CT2x    6       12.01100        0.000   A       0.358141284692  0.234304 ;
> partial charge def not found
> CT3x    6       12.01100        0.000   A       0.363486677001  0.326352 ;
> partial charge def not found
> H       1       1.008000        0.31    A       0.0400013524445 0.192464
>
>
> For atomtype CA does the sigma and epsilon parameters listed above
> correspond to individual CA atoms or is it between a pair?
>

Those are the epsilon and sigma values that get fed into the combination rule 
equation for any given pair, unless overriden by [ nonbond_params ] (i.e. CHARMM 
NBFIX).

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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